[BioC] Question regarding Installation of annotation package which was built using SQLforge (Suyog Pol)
Martin Morgan
mtmorgan at fhcrc.org
Sun Jan 31 20:05:54 CET 2010
Hi Suyong --
On 01/30/2010 03:49 PM, Suyog Pol wrote:
> HI
>
> Thank You Seth for your suggestion. I was able to install the Package
> using the following command.
>
> install.packages("illuminaHumanv3_ensemble_beta.db",
> repos = NULL, type = "source")
> However I am still unable to use the installed package. Although
> this time I am facing a different error
>
> I was applying the nsFilter from the genefilter library to filter my
> Expression set object eset. The eset was generated and used as follows:-
>
> dataMatrix <- exprs(eset.generated_using_lumi_package)
>
> #setting the rownames to the values which can be used by standard
> #package illuminaHumanv3
>
> rownames(dataMatrix) <- corrected.Probe_ID[1:48795]
>
> annotation <- 'illuminaHumanv3.ensemble.beta.db'
>
> eset <- new("ExpressionSet", exprs = dataMatrix ,
> annotation = 'illuminaHumanv3.ensemble.beta.db'
>
> library(genefilter)
> library("illuminaHumanv3.ensemble.beta.db") #The code for making and
> installing this package was discussed in my previous mail
> nsF <- nsFilter(eset, var.filter = FALSE)$eset
>
> I am getting the following error:-
>
>> nsF <- nsFilter(eset, var.filter = FALSE)$eset
> Error in get(mapName, envir = pkgEnv, inherits = FALSE) :
> object 'illuminaHumanv3.ensemble.beta_dbconn' not found
Are your names consistent, for instance below you use an underscore '_'
rather than a '.' to separate 'illuminaHumanv3' and 'ensemble'. It would
help to see, after loading your database, the output of
> search()
and
> ls("package:illuminaHumanv3.ensemble.beta.db")
Martin
>
> I was unable to figure out if this issue is related to procedure used for
> making the object or code for its installation.
>
> Your help will be much appreciated
>
> Suyog P
>
>
>> sessionInfo()
> R version 2.10.1 (2009-12-14)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] illuminaHumanv3.db_1.4.1
> [2] illuminaHumanv3.ensemble.beta.db_1.0.0
> [3] org.Hs.eg.db_2.3.6
> [4] genefilter_1.28.2
> [5] lumi_1.12.2
> [6] MASS_7.3-4
> [7] RSQLite_0.8-1
> [8] DBI_0.2-5
> [9] preprocessCore_1.8.0
> [10] mgcv_1.6-1
> [11] affy_1.24.2
> [12] annotate_1.24.1
> [13] AnnotationDbi_1.8.1
> [14] Biobase_2.6.1
>
> loaded via a namespace (and not attached):
> [1] affyio_1.14.0 grid_2.10.1 lattice_0.17-26
> Matrix_0.999375-33
> [5] nlme_3.1-96 splines_2.10.1 survival_2.35-7
> tools_2.10.1
> [9] xtable_1.5-6
>
>
>
>> Hi
>>
>> I have built an annotation package with the help of guidlines set in the
>> vignette/document
>> "SQLforge by Marc Carlson et al." I am having problem installing it.
>> The following code was used for building the package:-
>>
>> if(interactive()){
>> mart<- useMart("ensembl")
>> datasets<- listDatasets(mart)
>> mart<-useDataset("hsapiens_
>> gene_ensembl",mart)
>> ensemble.illumina<-
>> getBM(attributes=c("illumina_
> humanwg_6_v3","entrezgene"),filters="illumina_humanwg_6_v3",
>> values=illumina.humanv3.probeset, mart=mart,na.value = NA)
>>
>> }
>>
>> ##ensemble.Illumina was written into a file and modified to satisfy the
>> requisites of the input vector
>> ##required for the function makeDBPackage. The following code was used
> for
>> making the final
>> ##package:-
>>
>>> tmpout<- "Y:/path/to/annotation/package"
>>> library("human.db0")
>> Loading required package: AnnotationDbi
>> Loading .......
>>
>>> library("AnnotationDbi")
>>> makeDBPackage("HUMANCHIP_DB",
>> + affy=FALSE,
>> + prefix="illuminaHumanv3_ensemble_beta",
>> + fileName=filename,
>> + baseMapType="eg",
>> + outputDir = tmpout,
>> + version="1.0.0",
>> + manufacturer = "Illumina",
>> + chipName = "HT-12",
>> + manufacturerUrl = "http://www.illumina.com")
>> Loading required package: RSQLite
>> Loading required package: DBI
>> baseMapType is eg
>> Prepending Metadata
>> Creating Genes table
>> Appending Probes
>> Found 0 Probe Accessions
>> Appending Gene Info
>> Found 24758 Gene Names
>> Found 24758 Gene Symbols
>> Appending Chromosomes
>> Appending Cytogenetic Locations
>> Appending Omim
>> Appending RefSeq
>> Appending Pubmed
>> Appending Unigene
>> Appending ChrLengths
>> Appending 3 GO tables
>> Appending 3 GO ALL tables
>> Appending KEGG
>> Appending EC
>> Appending Chromosome Locations
>> Appending Pfam
>> Appending Prosite
>> Appending Alias
>> Appending Ensembl
>> Appending Uniprot
>> Appending Metadata
>>
>>
>> simplifying probes table
>> dropping redundant data
>> Creating package in
>> Y:/path/to/annotation/package/illuminaHumanv3_ensemble_beta.db
>>
>> #To install the above package : -
>>
>>>
>>
> install.packages("Y:/path/to/annotation/package/illuminaHumanv3_ensemble_beta.db",
>> + repos = NULL)
>> *Warning in install.packages("Y:/Genomics/ArrayData/Jan 2010 - CD140aO4
>> sorts/annotation/anno2/illuminaHumanv3_ensemble_beta.db", :
>> argument 'lib' is missing: using
>> 'C:\Users\suyogpol\Documents/R/win-library/2.10'
>> Error in gzfile(file, "r") : cannot open the connection
>> In addition: Warning messages:
>> 1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file
>> 2: In gzfile(file, "r") :
>> cannot open compressed file
>> 'illuminaHumanv3_ensemble_beta.db/DESCRIPTION', probable reason 'No such
>> file or directory*
>>
>> # I assumed that install.packages by default attempts to unzip the
> requested
>> package file
>> #To fix this I zipped the package directory and re used the
> install.packages
>> function:-
>>
>>
>>> setwd("Y:/path/to/annotation/package" )
>>> install.packages("illuminaHumanv3_ensemble_beta.db",
>> + repos = NULL)
>
> Can you please try again with:
>
>
> install.packages("illuminaHumanv3_ensemble_beta.db",
> repos = NULL, type = "source")
>
> I think that adding the type = "source" argument will get things going
> for you. If you want to be able to build package archives (.tar.gz as
> well as Windows binary packages .zip) you need to install Rtools (see R
> admin manual).
>
> + seth
>
>
> --
> Seth Falcon
> Bioconductor Core Team | FHCRC
>
> [[alternative HTML version deleted]]
>
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--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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